The purpose of this study was to investigate, characterize and map areas of the seabed of Las Perlas Archipelago (LPA), Republic of Panama using swath-bathymetry acoustic sonar techniques and to assess these methods as tools for feeding information into management zoning policy. In 2007 the LPA was granted conservation protection under national legislation. However, detailed management plans are still pending. Seabed mapping plays a fundamental role in identifying areas which should be prioritized within the management framework. Visual representation of habitat maps provides an effective medium for involving stakeholders in a co-management arena. In this survey, acoustically mapped areas of the seabed were ground-truthed using a combination of benthic grab samples, drop-down video and diver observations. The resulting mapped areas were then incorporated into a Geographic Information System (GIS) for further analysis. The output was a physical characterization of the seabed at three locations selected for being areas of high rugosity (habitat complexity) and, therefore, their potential importance as valuable fish aggregation sites. The rocky reefs and rhodolith beds identified in this survey represent particularly important fish aggregation and nursery habitats which should be considered priorities for protection under the management plans. This survey demonstrated the use of acoustic techniques to spatially resolve topographic features and physical characteristics of the seabed, illustrating their potential value as tools for fisheries management and marine reserve zoning in Las Perlas Archipelago and elsewhere. © 2010 Elsevier Ltd.